Although the technology to study microbial communities is available, it has yet to be applied comprehensively to the HIV-infected respiratory tract. Our central hypothesis is that the microbiome of the lung is shaped by HIV infection, the degree of HIV-mediated immunosuppression, and the use of antiretroviral and antimicrobial therapies. Furthermore, we hypothesize that the microbiome of the lung changes between periods of health and pneumonia, and that the presence of specific microbes or microbial onsortia within the lung is associated with the development of HIV-associated pulmonary complications and mortality. We propose a series of cross-sectional and longitudinal studies to characterize the bacterial, viral, and fungal microbiome present in the lungs of patients with acute and early HIV infection, chronic HIV infection, and opportunistic pneumonia. We propose to use three microarrays, the 16S rRNA PhyloChip, ViroChip, and 18S rRNA MycoChip as economical, standardized tools to provide a high resolution profile of the microbiome in a large number of HIV patient samples. To complement the microarray analysis and obtain functional profiles of microbial community behavior and associated host response, we will perform next generation 454- pyrosequencing of cDNA generated from a subset of these samples. These studies will be conducted within the Options, SCOPE, and IHOP cohorts, three established and well-characterized cohorts of HIV-infected and HIV-uninfected patients based at SFGH/UCSF. We propose the following specific aims: (1): To compare the lung microbiome in subjects with and without HIV infection; (2): To determine whether the degree of HIV-mediated immunosuppression (i.e., CD4 cell count) is related to the lung microbiome of HIV-infected subjects without acute illness/pneumonia; (3) To determine the effect of initiation of antiretroviral therapy and opportunistic pneumonia prophylaxis on the lung microbiome of HIV-infected subjects over time; (4) To determine the effects of opportunistic pneumonia and accompanying opportunistic pneumonia treatment on the lung microbiome of HIV-infected subjects over time; and (5) To correlate lung microbiome composition and function with HIV-associated morbidity and mortality.